Reconstructing and Using Phylogenies

Reconstructing and Using Phylogenies
16 Reconstructing and Using Phylogenies

Chapter 16 Reconstructing and Using Phylogenies
Key Concepts 16.1 All of Life Is Connected through Its Evolutionary History 16.2 Phylogeny Can Be Reconstructed from Traits of Organisms 16.3 Phylogeny Makes Biology Comparative and Predictive 16.4 Phylogeny Is the Basis of Biological Classification

Chapter 16 Opening Question
How are phylogenetic methods used to resurrect protein sequences from extinct organisms?

Concept 16.1 All of Life Is Connected through Its Evolutionary History
All of life is related through a common ancestor. This explains why the general principles of biology apply to all organisms. Phylogeny is the evolutionary history of these relationships. A phylogenetic tree is a diagrammatic reconstruction of that history.

An ancestor and its descendant populations form a lineage, shown as a line drawn on a time axis: PoL2e-ITA-Ch16-p0326-1R.jpg

When a single lineage divides into two, it is depicted as a split or node: PoL2e-ITA-Ch16-p0326-2R.jpg

As the lineages continue to split over time, the history can be represented in the form of a branching tree: PoL2e-ITA-Ch16-p jpg

A phylogenetic tree may portray the evolutionary history of: All life forms Major evolutionary groups Small groups of closely related species Individuals Populations Genes

The common ancestor of all the organisms in the tree forms the root of the tree: PoL2e-ITA-Ch16-p0326-4R.jpg

The timing of splitting events is shown by the position of nodes on a time axis. The splits represent events such as: A speciation event (for a tree of species) A gene duplication event (for a tree of genes) A transmission event (for a tree of viral lineages)

Vertical distances between branches do not have any meaning, and the vertical order of lineages is arbitrary. PoL2e-ITA-Ch16-p jpg

Taxon—any group of species that we designate with a name Clade—taxon that consists of all the evolutionary descendants of a common ancestor Identify a clade by picking any point on the tree and tracing all the descendant lineages.

Figure 16.1 Clades Represent All the Descendants of a Common Ancestor
Figure Clades Represent All the Descendants of a Common Ancestor All clades are subsets of larger clades, with all of life as the most inclusive taxon. In this example, the groups called mammals, amniotes, tetrapods, and vertebrates represent successively larger clades. Only a few species within each clade are represented on this tree. PoL2e-Fig jpg

Sister species: two species that are each other’s closest relatives Sister clades: any two clades that are each other’s closest relatives

Before the 1980s, phylogenetic trees were used mostly in evolutionary biology and systematics—the study and classification of biodiversity. Today trees are widely used in molecular biology, biomedicine, physiology, behavior, ecology, and virtually all other fields of biology.

Evolutionary relationships among species form the basis for biological classification. As new species are discovered, phylogenetic analyses are reviewed and revised. The tree of life’s evolutionary framework allows us to make predictions about the behavior, ecology, physiology, genetics, and morphology of species.

Homologous features are: Shared by two or more species Inherited from a common ancestor They can be any heritable traits, including DNA sequences, protein structures, anatomical structures, and behavior patterns.

Each character of an organism evolves from one condition (the ancestral trait) to another condition (the derived trait). Shared derived traits provide evidence of the common ancestry of a group and are called synapomorphies. The vertebral column is a synapomorphy of the vertebrates. The ancestral trait was an undivided supporting rod.

But similar traits can also develop in unrelated groups. Convergent evolution—when superficially similar traits evolve independently in different lineages

Figure 16.2 The Bones Are Homologous, the Wings Are Not
Figure The Bones Are Homologous, the Wings Are Not The supporting bone structures of both bat wings and bird wings are derived from a common tetrapod (four-limbed) ancestor and are thus homologous. However, the wings themselves—an adaptation for flight—evolved independently in the two groups. PoL2e-Fig R.jpg

In an evolutionary reversal, a character reverts from a derived state back to an ancestral state. These two types of traits are called homoplastic traits, or homoplasies. MEDIA CLIP 16.1 Morphing Arachnids

A trait may be ancestral or derived, depending on the point of reference. Example: Feathers are an ancestral trait for modern birds. But in a phylogeny of all living vertebrates, they are a derived trait found only in birds.

Concept 16.2 Phylogeny Can Be Reconstructed from Traits of Organisms
To construct a phylogenetic tree: Ingroup—the group of organisms of primary interest. Outgroup—species or group known to be closely related to, but phylogenetically outside of, the group of interest.

Table 16.1 PoL2e-Table jpg

A trait that is present in both the ingroup and the outgroup must have evolved before the origin of the ingroup and thus is ancestral for the ingroup. Traits present in only some members of the ingroup must be derived traits. APPLY THE CONCEPT: Phylogeny can be reconstructed from traits of organisms

Figure 16.3 Inferring a Phylogenetic Tree
Figure Inferring a Phylogenetic Tree This phylogenetic tree was constructed from the information given in Table 16.1 using the parsimony principle. Each clade in the tree is supported by at least one shared derived trait, or synapomorphy. PoL2e-Fig R.jpg

Parsimony principle—the preferred explanation of observed data is the simplest explanation In phylogenies, this means minimizing the number of evolutionary changes that need to be assumed over all characters in all groups. The best hypothesis is one that requires the fewest homoplasies.

Construction of phylogenetic trees has been revolutionized by computing technology and genome sequencing. Any trait that is genetically determined can be used in a phylogenetic analysis. Evidence comes from studies of morphology, development, the fossil record, behavioral traits, and molecular traits. ANIMATED TUTORIAL 16.1 Phylogeny and Molecular Evolution

Morphology: presence, size, shape, or other attributes of body parts Phylogenies of most extinct species depend almost exclusively on morphology. Fossils provide evidence that helps distinguish ancestral from derived traits. The fossil record can also reveal when lineages diverged.

Limitations of using morphology: Some taxa show few morphological differences. It is difficult to compare distantly related species. Some morphological variation is caused by environment.

Development: Similarities in developmental patterns may reveal evolutionary relationships. Example: The larvae of sea squirts have a notochord, which is also present in all vertebrates. This similarity is not apparent in adults. LINK: For more on the role of developmental processes in evolution, see Concepts 14.4 and 14.5

Figure 16.4 The Chordate Connection
Figure The Chordate Connection Embryonic development can offer vital clues to evolutionary relationships, since larvae sometimes share similarities that are not apparent in the adults. An example is the notochord, a synapomorphy of the chordates (a taxonomic group that includes the sea squirts as well as vertebrates such as frogs). All chordates have a notochord during their early development. The notochord is lost in adult sea squirts, whereas in adult frogs—as in all vertebrates—the vertebral column replaces the notochord as the body’s support structure. PoL2e-Fig R.jpg

Paleontology: The fossil record is an important source of information that helps distinguish ancestral from derived traits and timing of lineage splits. Limitations: Few or no fossils have been found for some groups. The fossil record for many groups is fragmentary.

Behavior: Some traits are cultural or learned and may not reflect evolutionary relationships (e.g., bird songs). Other traits have a genetic basis and can be used in phylogenies (e.g., frog calls).

Molecular data: DNA sequences have become the most widely used data for constructing phylogenetic trees. Nuclear, chloroplast, and mitochondrial DNA sequences are used. Information on gene products (such as amino acid sequences of proteins) are also used.

Mathematical models are now used to describe DNA changes over time. Models can account for multiple changes at a sequence position and different rates of change at different positions. Maximum likelihood methods identify the tree that most likely produced the observed data. They incorporate more information about evolutionary change than do parsimony methods.

Phylogenetic trees can be tested with computer simulations and by experiments on living organisms. These studies have confirmed the accuracy of phylogenetic methods and have been used to refine those methods and extend them to new applications. ANIMATED TUTORIAL 16.2 Using Phylogenetic Analysis to Reconstruct Evolutionary History

Figure 16.5 The Accuracy of Phylogenetic Analysis (Part 1)
Figure The Accuracy of Phylogenetic Analysis To test whether analysis of gene sequences can accurately reconstruct evolutionary history, we must have an unambiguously known phylogeny to compare against the reconstruction. Will the reconstruction match the observed phylogeny? PoL2e-Fig R.jpg

Concept 16.3 Phylogeny Makes Biology Comparative and Predictive
Applications of phylogenetic trees Reconstructing past events: In zoonotic diseases (infections transmitted to humans from another animal), it is important to understand when, where, and how the disease first entered a human population. One example is human immunodeficiency virus (HIV).

Phylogenies are important for understanding the present global diversity of HIV and determining the virus’s origins in human populations. Phylogenetic analysis shows that humans acquired HIV-1 from chimpanzees and HIV-2 from sooty mangabeys.

Figure 16.6 Phylogenetic Tree of Immunodeficiency Viruses
Figure Phylogenetic Tree of Immunodeficiency Viruses Immunodeficiency viruses have been transmitted to humans from two different simian hosts: HIV-1 from chimpanzees and HIV-2 from sooty mangabeys (the transmission events are marked by black diamonds). SIV stands for “simian immunodeficiency virus.” PoL2e-Fig R.jpg

Forensic investigations that involve viral transmission: A physician was accused of injecting blood from an HIV-positive patient into his former girlfriend in an attempt to kill her. Phylogenetic analysis revealed that the HIV strains present in the girlfriend were a subset of those present in the physician’s patient.

Figure 16.7 A Forensic Application of Phylogenetic Analysis
Figure A Forensic Application of Phylogenetic Analysis This phylogenetic analysis demonstrated that strains of HIV virus present in a victim (shown in red) were a phylogenetic subset of viruses isolated from a physician’s patient (shown in blue). This analysis was part of the evidence used to show that the physician drew blood from his HIV-positive patient and injected it into the victim in an attempt to kill her. The physician was found guilty of attempted murder by the jury. PoL2e-Fig R.jpg

Evolution of complex traits: Mail swordtail fish with longer tails are more likely to mate successfully. The sensory exploitation hypothesis suggests that female swordtails had a preference for males with long tails even before the tails evolved.

Phylogenetic analysis identified the closest relatives (Priapella), which do not have swords; but if a sword was attached artificially, females preferred that male.

Figure 16.8 The Origin of a Sexually Selected Trait
Figure The Origin of a Sexually Selected Trait The long tail of male swordtail fishes (genus Xiphophorus) apparently evolved through sexual selection, with females mating preferentially with males with a longer “sword.” Phylogenetic analysis reveals that the Priapella lineage split from the swordtails before the evolution of the sword. The independent finding that female Priapella prefer males with an artificial sword further supports the idea that this appendage evolved as a result of a preexisting preference in the females. PoL2e-Fig R.jpg

Revealing convergent evolution: Most flowering plants produce both male and female gametes on the same individual (in pollen and ovules). Self-incompatible species have mechanisms to prevent self-fertilization and must reproduce by outcrossing with another individual. Other species have self-fertilization, or selfing. LINK: Some mechanisms of self-incompatibility are discussed in Concept 27.1

Evolution of fertilization mechanisms was examined in the genus Leptosiphon. Phylogenetic analysis shows that self- compatibility evolved independently three times in the genus. Based on morphological similarities, the three species had been classified as one.

Figure 16.9 A Portion of the Leptosiphon Phylogeny
Figure A Portion of the Leptosiphon Phylogeny Self-compatibility (and flowers with short petals) evolved independently three times in this plant genus. Because the appearance and structure of the flowers converged in the three selfing lineages, taxonomists once mistakenly thought they were varieties of the same species. PoL2e-Fig R.jpg

Reconstructing ancestral states: Morphology, behavior, or nucleotide and amino acid sequences of ancestral species can be inferred. Example: Opsin proteins (pigments involved in vision) were reconstructed in the ancestral archosaur, and it was inferred that it was probably active at night.

Molecular clocks: Rates of molecular change are constant enough to predict the timing of lineage splits. A molecular clock uses the average rate at which a given gene or protein accumulates changes to gauge the time of divergence. They must be calibrated using independent data—the fossil record, known times of divergence, or biogeographic dates.

Figure 16.10 A Molecular Clock of the Protein Hemoglobin
Figure A Molecular Clock of the Protein Hemoglobin Amino acid replacements in hemoglobin have occurred at a relatively constant rate over nearly 500 million years of evolution. The graph shows the relationship between time of divergence and proportion of amino acid change for 13 pairs of vertebrate hemoglobin proteins. The average rate of change represents the molecular clock for hemoglobin in vertebrates. PoL2e-Fig R.jpg

A molecular clock was used to estimate the time when HIV-1 first entered human populations from chimpanzees. The clock was calibrated using biopsy samples taken in the 1980s and 1990s, then tested using samples from the 1950s. The common ancestor of this group of HIV-1 viruses can also be determined, with an estimated date of origin of about 1930.

Figure 16.11 Dating the Origin of HIV-1 in Human Populations (Part 1)
Figure Dating the Origin of HIV-1 in Human Populations (A) A phylogenetic analysis of the main group of HIV-1 viruses. The dates indicate the years in which samples were taken. (For clarity, only a small fraction of the samples that were examined in the original study are shown.) (B) A plot of year of isolation versus genetic divergence from the common ancestor provides an average rate of divergence, or a molecular clock. (C) The molecular clock is used to date a sample taken in 1959 (as a test of the clock) and the unknown date of origin of the HIV-1 main group (about 1930). Branch length from a common ancestor represents the average number of substitutions per nucleotide. PoL2e-Fig R.jpg

Figure 16.11 Dating the Origin of HIV-1 in Human Populations (Part 2)
Figure Dating the Origin of HIV-1 in Human Populations (A) A phylogenetic analysis of the main group of HIV-1 viruses. The dates indicate the years in which samples were taken. (For clarity, only a small fraction of the samples that were examined in the original study are shown.) (B) A plot of year of isolation versus genetic divergence from the common ancestor provides an average rate of divergence, or a molecular clock. (C) The molecular clock is used to date a sample taken in 1959 (as a test of the clock) and the unknown date of origin of the HIV-1 main group (about 1930). Branch length from a common ancestor represents the average number of substitutions per nucleotide. PoL2e-Fig R.jpg

Concept 16.4 Phylogeny Is the Basis of Biological Classification
The biological classification system was started by Swedish biologist Carolus Linnaeus in the 1700s. Binomial nomenclature gives every species a unique name consisting of two parts: the genus to which it belongs, and the species name. Example: Homo sapiens Linnaeus (Linnaeus is the person who first proposed the name)

Species and genera are further grouped into a hierarchical system of higher categories such as family—the taxon above genus. The family Hominidae contains humans, plus our recent fossil relatives, plus our closest living relatives, the chimpanzees and gorillas.

Families are grouped into orders Orders into classes Classes into phyla (singular phylum) Phyla into kingdoms The ranking of taxa within the Linnaean classification is subjective.

Linnaeus recognized the hierarchy of life, but he developed his system before evolutionary thought had become widespread. Biologists today often name taxa without placing them into the various Linnaean ranks. Evolutionary relationships are the basis for distinguishing, naming, and classifying biological groups.

Taxa should be monophyletic—containing an ancestor and all descendants of that ancestor, and no other organisms (a clade). A true monophyletic group can be removed from a phylogenetic tree by a single “cut.”

Figure 16.12 Monophyletic, Polyphyletic, and Paraphyletic Groups
Figure Monophyletic, Polyphyletic, and Paraphyletic Groups Monophyletic groups are the basis of biological taxa in modern classifications. Polyphyletic and paraphyletic groups do not accurately reflect evolutionary history. PoL2e-Fig R.jpg

But detailed phylogenetic information is not always available. Polyphyletic—a group that does not include its common ancestor Paraphyletic—a group that does not include all the descendants of a common ancestor These groups are inappropriate as taxonomic units because they do not correctly reflect evolutionary history. APPLY THE CONCEPT: Phylogeny is the basis of biological classification

Codes of biological nomenclature: Biologists around the world follow rules for the use of scientific names, to facilitate communication and dialogue. There may be many common names for one organism, or the same common name may refer to several species. But there is only one correct scientific name.

Figure 16.13 Same Common Name, Not the Same Species
Figure Same Common Name, Not the Same Species All three of these animals are known locally as anteaters. Unique scientific binomials allow biologists to communicate unambiguously about each species. (A) Myrmecophaga tridactyla, the giant anteater, searching for termites in Brazil. (B) Tachyglossus aculeatus, an echidna, is also called the spiny anteater. (C) Orycteropus afer, the aardvark, is also known as the Cape anteater. PoL2e-Fig jpg

Historically, scientists working with different groups of organisms developed different rules for classification, and sometimes name duplications occurred. Example: Drosophila is a genus of fruit flies and a genus of fungi. Today, biologists are working on a universal code of nomenclature that can be applied to all organisms.

Chapter 16 Answer to Opening Question
Biologists can reconstruct DNA and protein sequences of a clade’s ancestors if there is enough information about the genomes of their descendants. Real proteins that correspond to proteins in long-extinct species can be reconstructed. These techniques were used to reconstruct fluorescent proteins from the extinct ancestors of modern corals.

Figure 16.14 Evolution of Fluorescent Proteins of Corals
Figure Evolution of Fluorescent Proteins of Corals Mikhail Matz and his colleagues used phylogenetic analysis to reconstruct the sequences of extinct fluorescent proteins that were present in the ancestors of modern corals. They then expressed these proteins in bacteria and plated the bacteria in the form of a phylogenetic tree to show how the colors evolved over time. PoL2e-Fig R.jpg

Chapter 16 Answer to Opening Question
These methods rely on mathematical models that incorporate: Rates of replacement among different amino acid residues Substitution rates among nucleotides Changes in the rate of molecular evolution among different lineages

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